Unraveling the Genotypic and Phenotypic Diversity of the Psychrophilic Clostridium estertheticum Complex, a Meat Spoilage Agent

Abstract

The spoilage of vacuum-packed meat by Clostridium estertheticum complex (CEC), which is accompanied by or without production of copious amounts of gas, has been linked to the acetone–butyrate–ethanol fermentation, but the mechanism behind the variable gas production has not been fully elucidated. The reconstruction and comparison of intra- and interspecies metabolic pathways linked to meat spoilage at the genomic level can unravel the genetic basis for the variable phenotype. However, this is hindered by unavailability of CEC genomes, which in addition, has hampered the determination of genetic diversity and its drivers within CEC. Therefore, the current study aimed at determining the diversity of CEC through comprehensive comparative genomics. Fifty CEC genomes from 11 CEC species were compared. Recombination and gene gain/loss events were identified as important sources of natural variation within CEC, with the latter being pronounced in genomospecies2 that has lost genes related to flagellar assembly and signaling. Pan-genome analysis revealed variations in carbohydrate metabolic and hydrogenases genes within the complex. Variable inter- and intraspecies gas production in meat by C. estertheticum and Clostridium tagluense were associated with the distribution of the [NiFe]-hydrogenase hyp gene cluster whose absence or presence was associated with occurrence or lack of pack distention, respectively. Through comparative genomics, we have shown CEC species exhibit high genetic diversity that can be partly attributed to recombination and gene gain/loss events. We have also shown genetic basis for variable gas production in meat can be attributed to the presence/absence of the hyp gene cluster.

Phylogeny and Physiological Diversity of Cold-adapted Anaerobic Bacteria Isolated from Rice Field Soil in Japan

“…C. estertheticum is a psychrophilic anaerobe that causes BPS in vacuum-packed meat. C. estertheticum has often been isolated from or detected in meat or spoiled meat samples ( Cavill et al , 2011 ; Bonke et al , 2016 ; Wambui and Stephan, 2019 ; Zhang et al , 2019 ; Wambui et al , 2021 , 2022 ); however, the original environmental habitats or contamination routes of the bacterium to meat remain unclear ( Esteves et al , 2021 ). Although the closest relative of strain C5S18 was C. tagluense , which is phylogenetically included in the CEC group, the physiological characteristics of strain C5S18 or C. tagluense markedly differed from those of strain C5S7 or C. estertheticum ( Suetin et al , 2009 ).…”

“…Therefore, the distribution of anaerobic, psychrotrophic microbes in various environments is an important research subject for food microbiology ( Broda et al , 2009 ; Wambui and Stephan, 2019 ; Zhang et al , 2019 ; Wambui et al , 2020 ). The majority of psychrophilic Clostridium species are closely related to each other based on 16S rRNA gene sequence similarities and are called the Clostridium estertheticum complex (CEC) ( Wambui et al , 2021 , 2022 ). Although two subspecies names, C. estertheticum subsp.…”

Occurrence of vanHAX and Related Genes beyond the Actinobacteria Phylum

“…pfennigii DSM 3222, isolated from cattle rumen [ 82 ] (a biotope also inhabited by different actinobacteria [ 83 ]), and Cli. tagluense CS002—a causative agent of meat spoilage [ 84 ]. Although no MGE-related genes were discovered near van loci in Ox.…”

Rombocin, a Short Stable Natural Nisin Variant, Displays Selective Antimicrobial Activity against Listeria monocytogenes and Employs a Dual Mode of Action to Kill Target Bacterial Strains

“…Two strains, RC001 and RC002, were isolated anaerobically from chilled vacuum-packed meat as described in a previous study aimed at isolating and identifying Clostridium estertheticum complex (CEC) strains. 39 The strains could neither be identified as members CEC nor Clostridium sensu stricto group; hence, they were subjected to in silico-based identification methods as follows. Microbial genomic DNA was extracted from fresh cultures using the DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany).…”